OGO: an ontological approach for integrating knowledge about orthology

Miñarro-Gimenez Jose, Madrid Marisa, Fernandez-Breis, Fernandez-Breis Jesualdo

Description

There exist several information resources about orthology of genes and proteins, and there are also systems for querying those resources in an integrated way. However, caveats with current approaches include lack of integration, since results are shown sequentially by resource, meaning that there is redundant information and the users are required to combine the results obtained manually. Results In this paper we have applied the Ontological Gene Orthology approach, which makes use of a domain ontology to integrate the information output from selected orthology resources. The integrated information is stored in a knowledge base, which can be queried through semantic languages. A friendly user interface has been developed to facilitate the search; consequently, users do not need to have knowledge on ontologies or ontological languages to obtain the relevant information. Conclusion The development and application of our approach allows users to retrieve integrated results when querying orthology information, providing a gene product-oriented output instead of a traditional information resource-oriented one. Besides this benefit for users, it also allows a better exploitation and management of orthology information and knowledge.

Informations

• Publié par: biomed
• Publié le: 01 janvier 2009
• Nombre de lectures: 5
• Langue: English

Extrait

BMC Bioinformatics

BioMedCentral

Open Access Research OGO: an ontological approach for integrating knowledge about orthology 1 2 Jose Antonio MiñarroGimenez, Marisa Madridand 1 Jesualdo Tomas FernandezBreis*

1 2 Address: Departamentode Informática y Sistemas, Universidad de Murcia, Murcia, 30100, Spain andCell Division Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, M204BX, UK Email: Jose Antonio MiñarroGimenez  [e-mail]; Marisa Madrid  [e-mail]; Jesualdo Tomas FernandezBreis*  [e-mail] *Corresponding author

fromSemantic Web Applications and Tools for Life Sciences, 2008 Edinburgh, UK 28 November 2008

Published: 01 October 2009 BMC Bioinformatics2009,10(Suppl 10):S13

doi: 10.1186/1471210510S10S13

This article is available from: http://www.biomedcentral.com/14712105/10/S10/S13 ©2009 MiñarroGimenez et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract Background:There exist several information resources about orthology of genes and proteins, and there are also systems for querying those resources in an integrated way. However, caveats with current approaches include lack of integration, since results are shown sequentially by resource, meaning that there is redundant information and the users are required to combine the results obtained manually. Results:In this paper we have applied the Ontological Gene Orthology approach, which makes use of a domain ontology to integrate the information output from selected orthology resources. The integrated information is stored in a knowledge base, which can be queried through semantic languages. A friendly user interface has been developed to facilitate the search; consequently, users do not need to have knowledge on ontologies or ontological languages to obtain the relevant information. Conclusion:The development and application of our approach allows users to retrieve integrated results when querying orthology information, providing a gene productoriented output instead of a traditional information resourceoriented one. Besides this benefit for users, it also allows a better exploitation and management of orthology information and knowledge.

Background Traditionally, biological resources have been designed to be accessed and processed by humans. In such resources, data have been usually been represented in a non

standard format; consequently, data could not be managed and processed appropriately by computers. Hence, the representation of the information in a computer processable manner has become a major

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